No matter which way you choose, it will work out. The most important thing is do it while you can.
We did it in our 36 footer this past summer. No problems getting where we wanted to go. Just parked and drove the truck (or motorcycle) to other places we wanted to go. It was nice to have it to live in for the nearly 10 week trip, even though we didn't really spend a lot of time in it. Truck campers seem to be the RV of choice though for most up there, and a lot of them are rentals.
Some sections of road are bad, particularly the Alacan from the Canada border to Haines Junction. Mainly frost heaves, potholes and gravel breaks. You just need to go slow - like 40 or 45, when the roads get that bad and don't be in a hurry. Even did the Cassiar and the Top of the World Hwy with the 5er in tow. Worth it to do those once, but probably not twice. We didn't break anything other than a couple cracks to the truck windshield. The worst damage was my own fault raking a spruce down the side of the 5er at a campground. Took a lot of polishing with a buffer to get the scratches to almost disappear.
It took a couple weeks to get everything cleaned up when we got back. Mud was one thing, but the worst was driving on a 5 mile gravel break east of Whitehorse. It was real wet and muddy, but when we washed it up, we found out that they had laid down tar on the gravel and the whole 5th wheel was covered with specs of tar. Used a whole can of WD40, inch by inch, to get it all off.
We used styrofoam on the lower front of the 5er for rock protection and it worked out. If I do it again, I would get the rock flaps that mount on the truck receiver. Also, I would cover absolutely everything facing forward on the bottom of the 5er because the rocks knock a lot of paint off the fronts of the steps and bumper. I ended up just cleaning all those spots up and spray painting - looks like new.
Actually, looking at our 5er now, you would never know it has been to Alaska and back. Fuel costs were high, but between camping and fuel for 10 weeks from MI, we spent half of what a 2 week flight/cruise for 2 people costs. And we got to see pretty much everything we wanted to see and then some. So again, just do it!
We kept a blog of our trip here:
http://wheresdanneffel.blogspot.com/